SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

Abstract

We investigated SARS-CoV-2 potential tropism by surveying expression of viral entry-associated genes in single-cell RNA-sequencing data from multiple tissues from healthy human donors. We co-detected these transcripts in specific respiratory, corneal and intestinal epithelial cells, potentially explaining the high efficiency of SARS-CoV-2 transmission. These genes are co-expressed in nasal epithelial cells with genes involved in innate immunity, highlighting the cells' potential role in initial viral infection, spread and clearance. The study offers a useful resource for further lines of inquiry with valuable clinical samples from COVID-19 patients and we provide our data in a comprehensive, open and user-friendly fashion at www.covid19cellatlas.org.

Extended Data Fig. 1. Gene expression of ACE2 in an in vitro air-liquid interface (ALI) system

Epithelial regeneration system from nasal epithelial cells was used for in vitro cultures on successive days (7, 12 and 28), resulting in different epithelial cell types along differentiation trajectory characterized in Ruiz García et al. 2019. The cultures were differentiated in Pneumacult media. Schematic illustration depicts the respective cell types in the differentiation trajectory, and the dot plot illustrates the cultured cell types along the differentiation pseudotime, along with their respective location within the epithelial layers. For gene expression results in the dot plot: the dot size represents the proportion of cells within the respective cell type expressing the gene and the dot color represents the average gene expression level within the particular cell type.

Extended Data Fig. 2. Expression and co-expression of SARS-CoV-2 entry-associated proteases in ACE2⁺ airway epithelial cells

The expression of SARS-CoV-2 entry-associated proteases TMPRSS2, CTSB, and CTSL in ACE2⁺ cells from the Vieira Braga, Kar et al. (top) and Deprez et al. (bottom) airway epithelial datasets is shown. The color represents the expression level at the single-cell resolution and the cells are grouped based on the cell types specified.

Extended Data Fig. 3. Spearman’s correlation results from the two airway datasets are largely consistent.

a, Respiratory epithelial expression of the top 50 genes correlated with ACE2 expression based on Spearman’s correlation analysis performed on all cells within the Deprez et al. dataset. The colored gene names represent genes that are immune-associated (GO:0002376: immune system process). b, The Spearman’s correlation coefficients of gene expression with ACE2 from the Vieira Braga, Kar et al. airway epithelial dataset and the Deprez et al. airway dataset are shown in the scatter plot. The number of observations for the genes is counted in each bin, the value on the x-axis represents the Spearman’s correlation coefficients from the Vieira Braga, Kar et al. dataset, and the value on the y-axis represents the Spearman’s correlation coefficients from the Deprez et al. dataset.

Fig. 1|. Expression of ACE2 and TMPRSS2 across different tissues and its enrichment in nasal epithelial cells.

a, RNA expression of SARS-CoV-2 entry receptor ACE2 (first column), entry-associated protease TMPRSS2 (second column), and their co-expression (third column) from multiple scRNA-seq datasets across different tissues. Raw expression values were normalized, log transformed and summarized by published cell clustering where available, or reproduced clustering annotated using marker genes and cell type nomenclature from the respective studies. The size of the dots indicates the proportion of cells in the respective cell type having greater-than-zero expression of ACE2 (first column), TMPRSS2 (second column) or both (third column), while the colour indicates the mean expression of ACE2 (first and third columns) or TMPRSS2 (second column). b, Schematic illustration depicts the major anatomical regions in the human respiratory tree demonstrated in this study: nasal, lower airway, and lung parenchyma (left panel). Expression of ACE2 is from airway epithelial cell datasets: Vieira Braga, Kar et al. 2019 (middle panel) and Deprez et al. 2019 (right panel). The datasets were retrieved from existing sources, and the cell clustering and nomenclature were retained based on the respective studies. For gene expression results in the dot plots: the dot size represents the proportion of cells within the respective cell type expressing the gene and the dot color represents the average gene expression level within the particular cell type.

Fig. 2|. Respiratory expression of viral receptor/entry-associated genes and implications for viral transmissibility and genes associated with ACE2 expression.

a, Expression of ACE2 (an entry receptor for SARS-CoV and SARS-CoV-2), ANPEP (an entry receptor for HCoV-229E), ST6GAL1/ST3GAL4 (enzymes important for synthesis of influenza entry receptors), and DPP4 (an entry receptor for MERS-CoV) from the airway epithelial datasets: Vieira Braga, Kar et al. 2019 (left panel) and Deprez et al. 2019 (right panel). The basic reproductive number (R0) for respective viruses, if available, are shown. b, Respiratory epithelial expression of the top 50 genes correlated with ACE2 expression based on Spearman’s correlation analysis (with Benjamini-Hochberg-adjusted p-values) performed on all cells within the Vieira Braga, Kar et al. airway epithelial dataset. The colored gene names represent genes that are immune-associated (GO:0002376: immune system process or GO:0002526: acute inflammatory response). For gene expression results in the dot plots: the dot size represents the proportion of cells within the respective cell type expressing the gene and the color represents the average gene expression level within the particular cell type.